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acnr log file (check_x86_64_linux)

Tue May 10 13:40:38 2016: Checking package acnr (SVN revision 153) ...
* using log directory ‘/mnt/building/build_2016-05-10-12-11/RF_PKG_CHECK/PKGS/acnr.Rcheck’
* using R version 3.3.0 Patched (2016-05-09 r70593)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘acnr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘acnr’ version ‘0.2.5’
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: ‘Morgane Pierre-Jean ’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘R.utils’
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  acnr/inst/extdata/GSE13372/GenomeWideSNP_6/GSE13372,ASCRMAv2,HCC1143_GLEYSvsHCC1143BL_GLEYS,0,cnRegions.rds
  acnr/inst/extdata/GSE13372/GenomeWideSNP_6/GSE13372,ASCRMAv2,HCC1143_GLEYSvsHCC1143BL_GLEYS,100,cnRegions.rds

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘acnr’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'loadCnRegionData':
loadCnRegionData
  Code: function(dataSet = c("GSE29172", "GSE11976", "GSE13372"),
                 tumorFraction = 1)
  Docs: function(dataSet = c("GSE29172", "GSE11976"), tumorFraction =
                 1)
  Mismatches in argument default values:
    Name: 'dataSet' Code: c("GSE29172", "GSE11976", "GSE13372") Docs: c("GSE29172", "GSE11976")

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/mnt/building/build_2016-05-10-12-11/RF_PKG_CHECK/PKGS/acnr.Rcheck/00check.log’
for details.


Run time: 26.91 seconds.